Experiments on transfer learning architectures for biomedical relation extraction

Relation extraction (RE) consists in identifying and structuring automatically relations of interest from texts. Recently, BERT improved the top performances for several NLP tasks, including RE. However, the best way to use BERT, within a machine learning architecture, and within a transfer learning strategy is still an open question since it is highly dependent on each specific task and domain. Here, we explore various BERT-based architectures and transfer learning strategies (i.e., frozen or fine-tuned) for the task of biomedical RE on two corpora. Among tested architectures and strategies, our *BERT-segMCNN with finetuning reaches performances higher than the state-of-the-art on the two corpora (1.73 % and 32.77 % absolute improvement on ChemProt and PGxCorpus corpora respectively). More generally, our experiments illustrate the expected interest of fine-tuning with BERT, but also the unexplored advantage of using structural information (with sentence segmentation), in addition to the context classically leveraged by BERT.

Neural Network-based Word Alignment through Score Aggregation

We present a simple neural network for word alignment that builds source and target word window representations to compute alignment scores for sentence pairs. To enable unsupervised training, we use an aggregation operation that summarizes the alignment scores for a given target word. A soft-margin objective increases scores for true target words while decreasing scores for target words that are not present. Compared to the popular Fast Align model, our approach improves alignment accuracy by 7 AER on English-Czech, by 6 AER on Romanian-English and by 1.7 AER on English-French alignment.